Development of the next-generation GPU-based Monte Carlo simulation platform for radiation-induced DNA damage calculations

开发下一代基于 GPU 的蒙特卡罗模拟平台，用于辐射引起的 DNA 损伤计算

• 批准号: 10203527
• 负责人: Yujie Chi
• 金额: $ 44.66万
• 依托单位: UNIVERSITY OF TEXAS ARLINGTON
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-05-01 至 2025-04-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10203527
• 关键词: Address; Advanced Development; Affect; Biological; Biological Process; Biomedical Research; Cell Cycle; Chemicals; Clinical; Communities; Consumption; DNA; Data; Development; Diagnostic Imaging; Dose; Education; Educational process of instructing; Electrons; Ensure; Exhibits; Exposure to; G1 Phase; Geometry; Goals; Hispanic-serving Institution; Human; Industry; Ionizing radiation; Knowledge; Learning; Malignant Neoplasms; Mammography; Medical Imaging; Medicine; Metaphase; Methods; Microscopic; Military Personnel; Mission; Modality; Modeling; Modern Medicine; Monte Carlo Method; Organism; Outcome; Oxygen; Phase; Physics; Play; Polymers; Positron-Emission Tomography; Probability; Problem Solving; Process; Radiation; Radiation exposure; Radiation therapy; Radiosurgery; Research; Role; Shapes; Structure; Students; System; Technology; Testing; Therapeutic; Thoracic Radiography; Time; Uncertainty; Water; base; carcinogenicity; cost effective; design; experience; genotoxicity; imaging modality; improved; indexing; ionization; model development; molecular dynamics; multi-scale modeling; next generation; novel; open source; parallel computer; particle; repaired; simulation; spatiotemporal; success; tomography; tool; undergraduate student; user-friendly; web interface

Project Summary Ionizing radiation (IR) is a critical component of modern medicine. When IR penetrates through the organism, it could depart its energy to the medium mainly through ionization and excitation. The energy departure of IR is medium composition dependent, and hence it is used to ‘see’ the inner structure of the human beings, enabling the application of IR in the medical imaging of mammography, chest x-rays, computational tomography, positron emission tomography, etc. IR can also damage the structure and/or affect the function of the organism and hence it is applied to treat cancer in the form of radiosurgery and radiotherapy. Meanwhile, IR is found to be genotoxic and carcinogenic, calling the non-ending effort to understand the fundamental effects. Advanced cellular radiobiological study exhibited that the damage of deoxyribonucleic acid (DNA) plays a pivotal role towards the determination of the final biological or even clinical outcome after exposure to IR. It is hypothesized that when IR interacts with DNA, it could damage DNA in picoseconds by the primary and secondary IR particles and in microseconds by subsequently generated radiation radicals. It is then essential to understand how IR produces this initial damage under various radiation conditions. Microscopic Monte Carlo (MC) simulation such as Geant4-DNA, capable of computing this damaging process, has been playing an important role in the quantitative hypothesis-test. However, there are several issues in the state-of-the-art MC tools, making it hard to meet the increasing demanding for advanced applications. These include the low efficiency in dealing with the ‘many-body’ problem, the relatively large uncertainty in the final computing results, the lack of support for the entire cell cycle and the limited-access/user-unfriendly designs, etc. In this project, we propose to solve the above issues by developing a next-generation MC simulation tool for IR induced DNA damage computation through the novel implementations of graphical processing units (GPUs) parallel computing, the molecular dynamics/first principles based computation, the new DNA model development based on the extrusion model and polymer physics, and the open-source release with user-friendly interface. Upon success, the developed system is expected to serve as a next-generation simulation platform for the calculation of the initial DNA damage caused by IR, which can become a profound first-step towards a successful accomplishment of the “bottom-up” multi-scale modeling for the entire radiobiological process, making a significant impact in radiation medicine.

项目摘要 电离辐射（IR）是现代医学的关键组成部分。当IR穿过生物体时， 可以通过电离和兴奋将其能量主要出发到媒介。 IR的能量离开是 中等成分依赖于，因此它用于“看到”人类的内部结构，使得 IR在乳房X线摄影，胸部X射线，计算机断层扫描，正电子的医学成像中的应用 排放断层扫描等。IR还会损害生物体的结构和/或影响生物的功能，因此 它用于以放射外科手术和放射疗法的形式治疗癌症。同时，发现IR是基因研究 和致癌，称非终结努力来了解基本影响。 晚期细胞放射生物学研究表明，脱氧核糖核酸（DNA）的损伤起着关键 暴露于IR后，确定最终生物学甚至临床结果的作用。这是 假设IR与DNA相互作用时，它可能会损害原发性和 随后产生的辐射自由基在微秒内以及微秒中的次级IR颗粒。那是必不可少的 了解IR在各种辐射条件下如何产生这种初始损害。微观蒙特卡洛 （MC）能够计算此破坏过程的geant4-dna之类的模拟，一直在播放 在定量假设检验中的重要作用。但是，最新的MC中有几个问题 工具，很难满足对高级应用程序不断增长的要求。这些包括低 处理“多体”问题的效率，最终计算结果中相对较大的不确定性， 缺乏对整个单元格周期和有限访问/用户不友好的设计的支持，等等。 在这个项目中，我们建议通过为IR开发下一代MC模拟工具来解决上述问题 通过新颖的图形处理单元（GPU）实施的新实现诱导DNA损伤计算 平行计算，基于分子动力学/第一原理计算，新的DNA模型开发 基于扩展模型和聚合物物理，以及带有用户友好界面的开源释放。 成功后，预计开发的系统将作为下一代模拟平台 IR造成的初始DNA损伤的计算，这可能成为成功的第一步 完成整个放射生物学过程的“自下而上”多尺度建模，使 对放射医学的重大影响。